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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
GNU General Public License v3.0
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calculate the betweenness centrality as hubs #116

Closed Wensi13579 closed 4 months ago

Wensi13579 commented 4 months ago

What is the rationale behind the calculations for betweenness centrality as hubs? I specified hubPar = "betweenness" when running netAnalyze and obtained 116 hubs for each 5 conditions. However, when I checked the threshold for the exact value of betweenness centrality of each condition, it is approximately 0.005, and these values are all different. How is the threshold set?

stefpeschel commented 4 months ago

Have you left the hubQuant argument at 0.95? Then, hubs are the nodes with a betweenness centrality above the 95% quantile of the betweenness centrality values of all nodes. What threshold do you mean?

Wensi13579 commented 4 months ago

Thanks for your reply very much! I did not put this argument, but I found that there is a default setting for hubQuant = 0.95. Now I understand why that the cut-off of betweenness centrality value in each condition is different. The issue was resolved.